Actually my theory that this is the wheel sensor is that it is labeled "SPD". I thought that this was a sensor in the wheel that could be used for "dead reckoning" when the GPS signal is lost. This way it estimates your location on the map by using your speed/distance traveled, coupled with the gyro sensor that gives a relative bearing.

That brings up another question. That same diagnostic screen shows the relative bearing from the gyro sensor, but this never seems to match your compass heading. I am curious what this value is actually relative to. Is it relative to the direction you were going when you entered diagnostic mode, or is it relative to the direction you were going when you started out in (when you started the car)? I think it is the former, since the latter would be tricky if you started out in reverse...

I think that the speedo probably uses the input from this SPD sensor, but for some reason it is calibrated strangely to cause the low readings.

I recall reading somewhere about speedo error, and that European cars had their speedo calibrated in such a way that they NEVER read low, even if someone puts a huge set of wheels/tires on the vehicle. This is due to some European regulations that stipulate this "NEVER low" requirement. Perhaps Japan has a similar mandate? (I think this was from a Car and Driver editorial column a few years ago).